<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<title>MolTK C++ API: moltk/Alignment.hpp Source File</title>

<link href="tabs.css" rel="stylesheet" type="text/css"/>
<link href="doxygen.css" rel="stylesheet" type="text/css" />

<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/javascript">
  $(document).ready(function() { searchBox.OnSelectItem(0); });
</script>

</head>
<body>
<div id="top"><!-- do not remove this div! -->


<div id="titlearea">
<table cellspacing="0" cellpadding="0">
 <tbody>
 <tr style="height: 56px;">
  
  <td id="projectlogo"><img alt="Logo" src="moltk55.png"/></td>
  
  
  <td style="padding-left: 0.5em;">
   <div id="projectname">MolTK C++ API
   &#160;<span id="projectnumber">0.4.0</span>
   </div>
   
  </td>
  
  
  
 </tr>
 </tbody>
</table>
</div>

<!-- Generated by Doxygen 1.7.5.1 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
  <div id="navrow1" class="tabs">
    <ul class="tablist">
      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
      <li><a href="annotated.html"><span>Classes</span></a></li>
      <li class="current"><a href="files.html"><span>Files</span></a></li>
      <li>
        <div id="MSearchBox" class="MSearchBoxInactive">
        <span class="left">
          <img id="MSearchSelect" src="search/mag_sel.png"
               onmouseover="return searchBox.OnSearchSelectShow()"
               onmouseout="return searchBox.OnSearchSelectHide()"
               alt=""/>
          <input type="text" id="MSearchField" value="Search" accesskey="S"
               onfocus="searchBox.OnSearchFieldFocus(true)" 
               onblur="searchBox.OnSearchFieldFocus(false)" 
               onkeyup="searchBox.OnSearchFieldChange(event)"/>
          </span><span class="right">
            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
          </span>
        </div>
      </li>
    </ul>
  </div>
  <div id="navrow2" class="tabs2">
    <ul class="tablist">
      <li><a href="files.html"><span>File&#160;List</span></a></li>
      <li><a href="globals.html"><span>File&#160;Members</span></a></li>
    </ul>
  </div>
<div class="header">
  <div class="headertitle">
<div class="title">moltk/Alignment.hpp</div>  </div>
</div>
<div class="contents">
<a href="Alignment_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment">    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</span>
<a name="l00003"></a>00003 <span class="comment">    Copyright (C) 2011  Christopher M. Bruns</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">    This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">    it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">    the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00008"></a>00008 <span class="comment">    (at your option) any later version.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">    This program is distributed in the hope that it will be useful,</span>
<a name="l00011"></a>00011 <span class="comment">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00012"></a>00012 <span class="comment">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00013"></a>00013 <span class="comment">    GNU General Public License for more details.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">    You should have received a copy of the GNU General Public License along</span>
<a name="l00016"></a>00016 <span class="comment">    with this program; if not, write to the Free Software Foundation, Inc.,</span>
<a name="l00017"></a>00017 <span class="comment">    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
<a name="l00018"></a>00018 <span class="comment">    </span>
<a name="l00019"></a>00019 <span class="comment">    Commercial users should ask about our dual licensing model.</span>
<a name="l00020"></a>00020 <span class="comment">    For questions contact: cmbruns@rotatingpenguin.com</span>
<a name="l00021"></a>00021 <span class="comment">*/</span>
<a name="l00022"></a>00022 
<a name="l00023"></a>00023 <span class="preprocessor">#ifndef MOLTK_ALIGN_ALIGNMENT_H</span>
<a name="l00024"></a>00024 <span class="preprocessor"></span><span class="preprocessor">#define MOLTK_ALIGN_ALIGNMENT_H</span>
<a name="l00025"></a>00025 <span class="preprocessor"></span>
<a name="l00026"></a>00026 <span class="preprocessor">#include &quot;<a class="code" href="EString_8hpp.html">moltk/EString.hpp</a>&quot;</span>
<a name="l00027"></a>00027 <span class="preprocessor">#include &quot;<a class="code" href="Biosequence_8hpp.html">moltk/Biosequence.hpp</a>&quot;</span>
<a name="l00028"></a>00028 <span class="preprocessor">#include &quot;<a class="code" href="PDBStructure_8hpp.html">moltk/PDBStructure.hpp</a>&quot;</span>
<a name="l00029"></a>00029 <span class="preprocessor">#include &quot;<a class="code" href="Real_8hpp.html">moltk/Real.hpp</a>&quot;</span>
<a name="l00030"></a>00030 <span class="preprocessor">#include &quot;<a class="code" href="units_8hpp.html">moltk/units.hpp</a>&quot;</span>
<a name="l00031"></a>00031 <span class="preprocessor">#include &lt;iostream&gt;</span>
<a name="l00032"></a>00032 <span class="preprocessor">#include &lt;string&gt;</span>
<a name="l00033"></a>00033 <span class="preprocessor">#include &lt;vector&gt;</span>
<a name="l00034"></a>00034 
<a name="l00035"></a>00035 <span class="keyword">namespace </span>moltk {
<a name="l00036"></a>00036 
<a name="l00040"></a><a class="code" href="classmoltk_1_1Alignment.html">00040</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>
<a name="l00041"></a>00041 {
<a name="l00042"></a>00042 <span class="keyword">public</span>:
<a name="l00043"></a>00043 
<a name="l00044"></a>00044 
<a name="l00046"></a><a class="code" href="classmoltk_1_1Alignment.html#a6213f17d7957d5174e7af5627b649ac8">00046</a>     <span class="keyword">enum</span> <a class="code" href="classmoltk_1_1Alignment.html#a6213f17d7957d5174e7af5627b649ac8" title="Whether a particular Alignment member is a sequence or structure.">List</a> {
<a name="l00047"></a><a class="code" href="classmoltk_1_1Alignment.html#a6213f17d7957d5174e7af5627b649ac8a64315d2bea93b3770675d3a9bcbcfbbc">00047</a>         <a class="code" href="classmoltk_1_1Alignment.html#a6213f17d7957d5174e7af5627b649ac8a64315d2bea93b3770675d3a9bcbcfbbc">LIST_SEQUENCE</a>,
<a name="l00048"></a><a class="code" href="classmoltk_1_1Alignment.html#a6213f17d7957d5174e7af5627b649ac8a9532ce6c3a8fccfd79b37fe279e387e7">00048</a>         <a class="code" href="classmoltk_1_1Alignment.html#a6213f17d7957d5174e7af5627b649ac8a9532ce6c3a8fccfd79b37fe279e387e7">LIST_STRUCTURE</a>
<a name="l00049"></a>00049     };
<a name="l00050"></a>00050 
<a name="l00051"></a><a class="code" href="classmoltk_1_1Alignment.html#a3743461184a4c55f0e54e6ade1e9ef68">00051</a>     <span class="keyword">typedef</span> <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">moltk::EString</a> <a class="code" href="classmoltk_1_1Alignment.html#a3743461184a4c55f0e54e6ade1e9ef68">EString</a>;
<a name="l00052"></a>00052 
<a name="l00054"></a><a class="code" href="classmoltk_1_1Alignment_1_1Row.html">00054</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1Alignment_1_1Row.html" title="Meta-data for one sequence in an Alignment.">Row</a>
<a name="l00055"></a>00055     {
<a name="l00056"></a>00056     <span class="keyword">public</span>:
<a name="l00057"></a><a class="code" href="classmoltk_1_1Alignment_1_1Row.html#ad0b7b0fe65a48851cfa0e69e50153d2c">00057</a>         <a class="code" href="classmoltk_1_1Alignment.html#a6213f17d7957d5174e7af5627b649ac8" title="Whether a particular Alignment member is a sequence or structure.">List</a> <a class="code" href="classmoltk_1_1Alignment_1_1Row.html#ad0b7b0fe65a48851cfa0e69e50153d2c">list</a>; <span class="comment">// which list: sequences or structures?</span>
<a name="l00058"></a><a class="code" href="classmoltk_1_1Alignment_1_1Row.html#a6cf75dce3ed389af8aad0610900658e8">00058</a>         <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1Alignment_1_1Row.html#a6cf75dce3ed389af8aad0610900658e8">list_index</a>;
<a name="l00059"></a><a class="code" href="classmoltk_1_1Alignment_1_1Row.html#a4fec4a1fd2d57745a431a9a27482fa8f">00059</a>         <a class="code" href="namespacemoltk.html#afe6fbd8f5686b34143c2742fcc97292c" title="Real represents a real number, such as 5.6.">Real</a> <a class="code" href="classmoltk_1_1Alignment_1_1Row.html#a4fec4a1fd2d57745a431a9a27482fa8f">sequence_weight</a>;
<a name="l00060"></a><a class="code" href="classmoltk_1_1Alignment_1_1Row.html#a2b0445bd2200448dcb39596a462c58e5">00060</a>         <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a> <a class="code" href="classmoltk_1_1Alignment_1_1Row.html#a2b0445bd2200448dcb39596a462c58e5">e_string</a>;
<a name="l00061"></a>00061     };
<a name="l00062"></a>00062 
<a name="l00063"></a>00063 
<a name="l00064"></a>00064 <span class="keyword">public</span>:
<a name="l00065"></a>00065     <a class="code" href="classmoltk_1_1Alignment.html#a32d343d192cf39cb0f0968e26223af78">Alignment</a>();
<a name="l00066"></a>00066     <span class="comment">/* implicit */</span> <a class="code" href="classmoltk_1_1Alignment.html#a32d343d192cf39cb0f0968e26223af78">Alignment</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Biosequence.html" title="A macromolecule sequence (DNA or RNA or protein)">Biosequence</a>&amp; sequence);
<a name="l00067"></a>00067     <span class="comment">/* implicit */</span> <a class="code" href="classmoltk_1_1Alignment.html#a32d343d192cf39cb0f0968e26223af78">Alignment</a>(<span class="keyword">const</span> std::string&amp; alignment_string);
<a name="l00068"></a>00068     <span class="comment">/* implicit */</span> <a class="code" href="classmoltk_1_1Alignment.html#a32d343d192cf39cb0f0968e26223af78">Alignment</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* alignment_string);
<a name="l00069"></a>00069     <span class="comment">// explicit Alignment(std::istream&amp; is);</span>
<a name="l00070"></a><a class="code" href="classmoltk_1_1Alignment.html#a7707218270b81f730c8be5d19763dc22">00070</a>     <a class="code" href="classmoltk_1_1Alignment.html#a7707218270b81f730c8be5d19763dc22">~Alignment</a>() {}
<a name="l00071"></a>00071     <a class="code" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp; <a class="code" href="classmoltk_1_1Alignment.html#ad319bf0e8fdcb7b2de65fd7d03c7261d">append_sequence</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Biosequence.html" title="A macromolecule sequence (DNA or RNA or protein)">Biosequence</a>&amp; sequence);
<a name="l00072"></a>00072     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment.html#a1744a2bb15a68fd5eee6ad9f457f186f">load_string</a>(<span class="keyword">const</span> std::string&amp; alignment_string);
<a name="l00073"></a>00073     <a class="code" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp; <a class="code" href="classmoltk_1_1Alignment.html#a9fc6acdad2f8dc2e9a070b39dd391533">load_fasta</a>(std::istream&amp; input_stream);
<a name="l00074"></a>00074     <a class="code" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp; <a class="code" href="classmoltk_1_1Alignment.html#a9fc6acdad2f8dc2e9a070b39dd391533">load_fasta</a>(<span class="keyword">const</span> std::string&amp; file_name);
<a name="l00075"></a>00075 
<a name="l00076"></a>00076     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment.html#a49b02248c0a05137369e26d826b9075f">write_pretty</a>(std::ostream&amp; output_stream) <span class="keyword">const</span>;
<a name="l00077"></a>00077     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment.html#a49b02248c0a05137369e26d826b9075f">write_pretty</a>(<span class="keyword">const</span> std::string&amp; file_name) <span class="keyword">const</span>;
<a name="l00078"></a>00078     std::string <a class="code" href="classmoltk_1_1Alignment.html#a2574c152a5662243f4626d4bb0de1ed3">pretty</a>() <span class="keyword">const</span>;
<a name="l00079"></a>00079 
<a name="l00080"></a>00080     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment.html#a60122a64be28573829c1a956737c8c11">write_fasta</a>(std::ostream&amp; output_stream) <span class="keyword">const</span>;
<a name="l00081"></a>00081     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment.html#a60122a64be28573829c1a956737c8c11">write_fasta</a>(<span class="keyword">const</span> std::string&amp; file_name) <span class="keyword">const</span>;
<a name="l00082"></a>00082     std::string <a class="code" href="classmoltk_1_1Alignment.html#a338529e9299d91018d134b130b26a6dd">fasta</a>() <span class="keyword">const</span>;
<a name="l00083"></a>00083 
<a name="l00084"></a>00084     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment.html#a1ade7cd4b169cbf8bc72504cd973a13f">write_id_table</a>(std::ostream&amp; output_stream) <span class="keyword">const</span>;
<a name="l00085"></a>00085     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1Alignment.html#a1ade7cd4b169cbf8bc72504cd973a13f">write_id_table</a>(<span class="keyword">const</span> std::string&amp; file_name) <span class="keyword">const</span>;
<a name="l00086"></a>00086     std::string <a class="code" href="classmoltk_1_1Alignment.html#adc61d7c6de21d88523c96423b2b1f408">id_table</a>() <span class="keyword">const</span>;
<a name="l00087"></a>00087 
<a name="l00088"></a>00088     <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1Alignment.html#a628e15ff3478f591868bc1465109b04d">get_number_of_columns</a>() <span class="keyword">const</span>;
<a name="l00089"></a>00089     <span class="comment">// get_number_of_sequences() includes both sequences and structures</span>
<a name="l00090"></a><a class="code" href="classmoltk_1_1Alignment.html#a2486341695c895251bd124357a21371c">00090</a>     <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1Alignment.html#a2486341695c895251bd124357a21371c">get_number_of_sequences</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Alignment.html#a4bac71883cd63ec6b766497640684a81">rows</a>.size();}
<a name="l00091"></a>00091     <a class="code" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a> <a class="code" href="classmoltk_1_1Alignment.html#a85b58270d404b46f62fc7eeed7e2b105">align</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp;, <span class="keyword">const</span> <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>&amp;, <span class="keyword">const</span> <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>&amp;) <span class="keyword">const</span>;
<a name="l00092"></a><a class="code" href="classmoltk_1_1Alignment.html#aa27d71c83a6cb5d0584e9db931119045">00092</a>     <span class="keyword">const</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html" title="Parent class for macromolecule sequences and structures.">BaseBiosequence</a>&amp; <a class="code" href="classmoltk_1_1Alignment.html#aa27d71c83a6cb5d0584e9db931119045">get_sequence</a>(<span class="keywordtype">size_t</span> index)<span class="keyword"> const</span>
<a name="l00093"></a>00093 <span class="keyword">    </span>{
<a name="l00094"></a>00094         <span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment_1_1Row.html" title="Meta-data for one sequence in an Alignment.">Row</a>&amp; row = <a class="code" href="classmoltk_1_1Alignment.html#a4bac71883cd63ec6b766497640684a81">rows</a>[index];
<a name="l00095"></a>00095         <span class="keywordflow">if</span> (row.<a class="code" href="classmoltk_1_1Alignment_1_1Row.html#ad0b7b0fe65a48851cfa0e69e50153d2c">list</a> == <a class="code" href="classmoltk_1_1Alignment.html#a6213f17d7957d5174e7af5627b649ac8a64315d2bea93b3770675d3a9bcbcfbbc">LIST_SEQUENCE</a>)
<a name="l00096"></a>00096             <span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Alignment.html#a78aa4d5f29a114e1a58b7f32eb98e24d">sequences</a>[row.<a class="code" href="classmoltk_1_1Alignment_1_1Row.html#a6cf75dce3ed389af8aad0610900658e8">list_index</a>];
<a name="l00097"></a>00097         <span class="keywordflow">else</span>
<a name="l00098"></a>00098             <span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Alignment.html#aa6fde73aa22498189439380b2a245f37">structures</a>[row.<a class="code" href="classmoltk_1_1Alignment_1_1Row.html#a6cf75dce3ed389af8aad0610900658e8">list_index</a>];
<a name="l00099"></a>00099     }
<a name="l00100"></a><a class="code" href="classmoltk_1_1Alignment.html#a68e0607cad31d5eec46b90d81c62eed2">00100</a>     <span class="keyword">const</span> <a class="code" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>&amp; <a class="code" href="classmoltk_1_1Alignment.html#a68e0607cad31d5eec46b90d81c62eed2">get_estring</a>(<span class="keywordtype">size_t</span> index)<span class="keyword"> const</span>
<a name="l00101"></a>00101 <span class="keyword">    </span>{
<a name="l00102"></a>00102         <span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Alignment.html#a4bac71883cd63ec6b766497640684a81">rows</a>[index].e_string;
<a name="l00103"></a>00103     }
<a name="l00104"></a><a class="code" href="classmoltk_1_1Alignment.html#abde767106550bdb46c923146b3629c2f">00104</a>     <span class="keyword">const</span> <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">moltk::units::Information</a>&amp; <a class="code" href="classmoltk_1_1Alignment.html#abde767106550bdb46c923146b3629c2f">score</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Alignment.html#ad7f4499388720ae855277fe046bbea44">m_score</a>;}
<a name="l00105"></a><a class="code" href="classmoltk_1_1Alignment.html#a110d140d99982b84a8545a23d51b8543">00105</a>     <a class="code" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp; <a class="code" href="classmoltk_1_1Alignment.html#a110d140d99982b84a8545a23d51b8543">set_score</a>(<span class="keyword">const</span> <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">moltk::units::Information</a>&amp; s) 
<a name="l00106"></a>00106     {
<a name="l00107"></a>00107         <a class="code" href="classmoltk_1_1Alignment.html#ad7f4499388720ae855277fe046bbea44">m_score</a> = s;
<a name="l00108"></a>00108         <span class="keywordflow">return</span> *<span class="keyword">this</span>;
<a name="l00109"></a>00109     }
<a name="l00110"></a>00110 
<a name="l00111"></a><a class="code" href="classmoltk_1_1Alignment.html#a5c933bbcecb2459310f897119f11fda7">00111</a>     <span class="keyword">inline</span> <span class="keyword">friend</span> std::ostream&amp; <a class="code" href="classmoltk_1_1Alignment.html#a5c933bbcecb2459310f897119f11fda7">operator&lt;&lt;</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp; ali)
<a name="l00112"></a>00112     {
<a name="l00113"></a>00113         ali.<a class="code" href="classmoltk_1_1Alignment.html#a49b02248c0a05137369e26d826b9075f">write_pretty</a>(os);
<a name="l00114"></a>00114         <span class="keywordflow">return</span> os;
<a name="l00115"></a>00115     }
<a name="l00116"></a>00116 
<a name="l00117"></a>00117 
<a name="l00118"></a>00118 <span class="keyword">protected</span>:
<a name="l00119"></a><a class="code" href="classmoltk_1_1Alignment.html#a78aa4d5f29a114e1a58b7f32eb98e24d">00119</a>     std::vector&lt;Biosequence&gt; <a class="code" href="classmoltk_1_1Alignment.html#a78aa4d5f29a114e1a58b7f32eb98e24d">sequences</a>;
<a name="l00120"></a><a class="code" href="classmoltk_1_1Alignment.html#aa6fde73aa22498189439380b2a245f37">00120</a>     std::vector&lt;PDBStructure::Chain&gt; <a class="code" href="classmoltk_1_1Alignment.html#aa6fde73aa22498189439380b2a245f37">structures</a>;
<a name="l00121"></a><a class="code" href="classmoltk_1_1Alignment.html#a4bac71883cd63ec6b766497640684a81">00121</a>     std::vector&lt;Row&gt; <a class="code" href="classmoltk_1_1Alignment.html#a4bac71883cd63ec6b766497640684a81">rows</a>;
<a name="l00122"></a><a class="code" href="classmoltk_1_1Alignment.html#ad7f4499388720ae855277fe046bbea44">00122</a>     <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">moltk::units::Information</a> <a class="code" href="classmoltk_1_1Alignment.html#ad7f4499388720ae855277fe046bbea44">m_score</a>;
<a name="l00123"></a><a class="code" href="classmoltk_1_1Alignment.html#adf2beb6028be5a2ab437bb93aff90b61">00123</a>     <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1Alignment.html#adf2beb6028be5a2ab437bb93aff90b61">pretty_width</a>;
<a name="l00124"></a>00124 };
<a name="l00125"></a>00125 
<a name="l00129"></a>00129 <a class="code" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a> <a class="code" href="namespacemoltk.html#a5d6a32006fb76447d32cde962b6ab1fb" title="global load_fasta method helps get SEQUOIA-like conciseness in python.">load_fasta</a>(<span class="keyword">const</span> std::string&amp; file_name);
<a name="l00130"></a>00130 
<a name="l00131"></a>00131 } <span class="comment">// namespace moltk</span>
<a name="l00132"></a>00132 
<a name="l00133"></a>00133 
<a name="l00134"></a>00134 <span class="preprocessor">#endif // MOLTK_ALIGN_ALIGNMENT_H</span>
</pre></div></div>
</div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
     onmouseover="return searchBox.OnSearchSelectShow()"
     onmouseout="return searchBox.OnSearchSelectHide()"
     onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Friends</a></div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0" 
        name="MSearchResults" id="MSearchResults">
</iframe>
</div>



<hr class="footer"/><address class="footer"><small>
Generated by &#160;<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.7.5.1
</small></address>

</body>
</html>
